diff --git a/Makefile b/Makefile
index a37180bd..f2aa2aa6 100644
--- a/Makefile
+++ b/Makefile
@@ -19,7 +19,10 @@ BOARD		?= qemu
 # If musl-libc is being used in the initrd, set the heads_cc
 # variable to point to it.
 musl_dep	:= musl
-heads_cc	:= $(INSTALL)/bin/musl-gcc
+heads_cc	:= $(INSTALL)/bin/musl-gcc \
+	-fdebug-prefix-map=$(pwd)=heads \
+	-gno-record-gcc-switches \
+
 #heads_cc	:= $(HOME)/install/x86_64-linux-musl/x86_64-linux-musl/bin/gcc
 
 all: $(BOARD).rom
diff --git a/modules/cryptsetup b/modules/cryptsetup
index dd4015e3..81748c2d 100644
--- a/modules/cryptsetup
+++ b/modules/cryptsetup
@@ -8,18 +8,23 @@ cryptsetup_tar := cryptsetup-$(cryptsetup_version).tar.xz
 cryptsetup_url := https://www.kernel.org/pub/linux/utils/cryptsetup/v1.7/cryptsetup-$(cryptsetup_version).tar.xz
 cryptsetup_hash := af2b04e8475cf40b8d9ffd97a1acfa73aa787c890430afd89804fb544d6adc02
 
+# Use an empty prefix so that the executables will not include the
+# build path.
 cryptsetup_configure := ./configure \
 	CC="$(heads_cc)" \
-	CFLAGS="-I$(INSTALL)/include" \
-	LDFLAGS="-L$(INSTALL)/lib" \
 	--host i386-elf-linux \
-	--prefix "$(INSTALL)" \
+	--prefix "" \
 	--disable-gcrypt-pbkdf2 \
 	--with-crypto_backend=kernel \
 
+# but after building, replace prefix so that they will be installed
+# in the correct directory.
 cryptsetup_target := \
 	-j 8 \
-	install
+	&& $(MAKE) \
+		-C $(build)/$(cryptsetup_dir) \
+		prefix="$(INSTALL)" \
+		install
 
 cryptsetup_output := \
 	src/.libs/cryptsetup \
diff --git a/modules/gpg b/modules/gpg
index 6ca97e61..ac499057 100644
--- a/modules/gpg
+++ b/modules/gpg
@@ -8,10 +8,15 @@ gpg_tar := gnupg-$(gpg_version).tar.bz2
 gpg_url := https://www.gnupg.org/ftp/gcrypt/gnupg/$(gpg_tar)
 gpg_hash := 6b47a3100c857dcab3c60e6152e56a997f2c7862c1b8b2b25adf3884a1ae2276
 
+# For reproducibility reasons we have to override the exec_prefix
+# and datarootdir on the configure line so that the Makefiles will
+# be generated with the correct paths, but then re-write them when
+# we use the install target so that they will be copied to the correct
+# location.
 gpg_configure := ./configure \
 	CC="$(heads_cc)" \
 	--host i386-elf-linux \
-	--prefix $(INSTALL) \
+	--prefix "" \
 	--disable-bzip2 \
 	--disable-gpg \
 	--disable-gpgsm \
@@ -32,7 +37,14 @@ gpg_configure := ./configure \
 	--disable-dns-cert \
 	--disable-regex \
 
-gpg_target := -j 8 install
+# Run one build to generate the executables with the pre-defined
+# exec_prefix and datarootdir, then a second make to install the binaries
+# into our actual target location
+gpg_target := -j 8 \
+	&& $(MAKE) -C $(build)/$(gpg_dir) \
+		exec_prefix=$(pwd)/install \
+		datarootdir=$(pwd)/install/share \
+		install
 
 gpg_output := g10/gpgv
 
diff --git a/modules/libuuid b/modules/libuuid
index 5ab2c3a8..855a9908 100644
--- a/modules/libuuid
+++ b/modules/libuuid
@@ -8,10 +8,14 @@ libuuid_hash := 46af3275291091009ad7f1b899de3d0cea0252737550e7919d17237997db5644
 
 libuuid_configure := ./configure \
 	CC="$(heads_cc)" \
-	--prefix $(INSTALL) \
+	--prefix "" \
 	--host i386-elf-linux \
 
-libuuid_target := install
+libuuid_target := -j 8 && \
+	$(MAKE) \
+		-C "$(build)/$(libuuid_dir)" \
+		prefix="$(INSTALL)" \
+		install
 
 libuuid_libraries := .libs/libuuid.so
 libuuid_depends := $(musl_dep)
diff --git a/modules/popt b/modules/popt
index a8468eb3..9803bec3 100644
--- a/modules/popt
+++ b/modules/popt
@@ -8,10 +8,14 @@ popt_hash := e728ed296fe9f069a0e005003c3d6b2dde3d9cad453422a10d6558616d304cc8
 
 popt_configure := ./configure \
 	CC="$(heads_cc)" \
-	--prefix $(INSTALL) \
+	--prefix "" \
 	--host i386-elf-linux \
 
-popt_target := install
+popt_target := -j 8 \
+	&& $(MAKE) \
+		-C "$(build)/$(popt_dir)" \
+		prefix="$(INSTALL)" \
+		install
 
 popt_libraries := ./libs/libpopt.so
 popt_depends := $(musl_dep)
diff --git a/modules/qrencode b/modules/qrencode
index 8f0ab135..8f1ae921 100644
--- a/modules/qrencode
+++ b/modules/qrencode
@@ -10,10 +10,14 @@ qrencode_output := .libs/libqrencode.so.$(qrencode_version)
 
 qrencode_configure := ./configure \
 	CC="$(heads_cc)" \
-	--prefix $(INSTALL) \
+	--prefix "" \
 	--without-tools \
 	--host i386-elf-linux \
 
-qrencode_target := install
+qrencode_target := -j 8 \
+	&& $(MAKE) \
+		-C "$(build)/$(qrencode_dir)" \
+		prefix="$(INSTALL)" \
+		install
 
 qrencode_depends := $(musl_dep)